The fields of forensics, paternity testing, cell line ID, and personalized medicine routinely use DNA-based techniques for identity determinations, genotyping, phenotypic prediction, and in the prediction and/or prevention of disease. DNA typing involves the analysis of select regions of genomic DNA, commonly referred to as “markers.” Most typing methods in use today are specifically designed to detect and analyze differences in the length and/or sequence of one or more regions of DNA markers known to appear in at least two different forms in a population. Such length and/or sequence variation is referred to as “polymorphism.” Any region (i.e., “locus”) of DNA in which such a variation occurs is referred to as a “polymorphic locus.”
In recent years, the discovery and development of polymorphic short tandem repeats (STRs) as genetic markers has played an important role in DNA typing. STRs have become the primary means for human identity and forensic DNA testing.
In particular, Y-STR analysis is a valuable tool in a number of applications. Forensic applications include use in investigation of sexual assault cases where male DNA may be present in a sample that also contains an excess of female DNA. Y-STR analysis can be critical in excluding individuals from further inquiries. In another forensic application, a sample may include DNA from multiple male contributors. Y-STR analysis can be used to trace family relationship among males, either in forensic or other inheritance analyses, and can be used in missing person investigations. Additionally, Y-STR analysis can be used in paternity testing, including scenarios where the alleged father is not available for direct comparison.
One database used to assist investigators is the U.S. Y-STR Database, a searchable listing of 11- to 23-locus Y-STR haplotypes. The database is funded by the National Institute of Justice and managed by the National Center for Forensic Science (NCFS) in conjunction with the University of Central Florida. The U.S. Y-STR Database is a population database only and is intended for use in estimating Y-STR haplotype population frequencies for forensic case work purposes.
Several limitations exist for currently available Y-STR analysis kits. While haplotype databases are used to establish the frequency of a haplotype in specific populations, haplotype resolution (HR) of kits may vary across populations (Vermeulen et al., (2009) FSIG 3:205-213). Secondly, using current kits, a male relative of a suspected individual may not be excluded. Relatives separated by up to 20 generations may have Y-STR profiles indistinguishable from each other, according to current analyses (Ballantyne et al. (2010): Am J Hum Genet 87:341-353). Thirdly, adventitious matches increase as more male profiles are added to Y-STR frequency databases. Therefore, there exists a need in the art, to improve Y-STR multiplex analysis systems, assays, kits, and methods.